Contacts of the helix formed by residues 355 - 372 (chain B) in PDB entry 1KI6
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with PRO 355 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46B MET* 5.4 7.4 - - + -
47B PRO* 3.9 30.7 - - + +
353B THR 4.9 0.9 - - - +
354B THR* 1.3 89.0 - - + +
356B GLY* 1.3 56.3 + - - +
357B SER 3.1 5.2 + - - -
358B ILE* 3.3 24.1 + - - +
359B PRO* 3.6 1.9 - - - +
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Residues in contact with GLY 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354B THR* 2.9 11.9 - - - +
355B PRO* 1.3 79.7 - - - +
357B SER* 1.3 53.7 + - - -
358B ILE 3.3 0.7 - - - -
359B PRO* 3.3 18.1 - - - +
360B THR* 2.7 27.9 + - - -
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Residues in contact with SER 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142B HIS* 3.0 33.0 - - - -
352B VAL* 3.5 18.4 - - - -
353B THR 3.8 2.1 + - - -
354B THR* 2.7 46.5 + - - -
356B GLY* 1.3 77.2 - - - +
358B ILE* 1.3 57.7 + - - +
360B THR* 3.2 1.3 + - - -
361B ILE* 2.8 40.5 + - - +
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Residues in contact with ILE 358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B PRO* 3.8 24.0 - - + -
48B THR 4.1 17.3 - - - +
49B LEU* 4.9 1.8 - - + -
156B ALA* 4.2 13.2 - - + +
157B LEU* 3.6 41.5 - - + +
352B VAL* 4.2 17.5 - - + -
355B PRO 3.6 10.3 - - - +
357B SER* 1.3 78.6 - - - +
359B PRO* 1.3 72.3 - - + +
361B ILE* 3.3 4.2 + - + +
362B CYS* 3.0 22.2 + - - +
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Residues in contact with PRO 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355B PRO 3.6 4.0 - - - +
356B GLY* 3.3 24.5 - - - +
358B ILE* 1.3 98.5 - - + +
360B THR* 1.3 55.7 + - - +
362B CYS* 3.0 10.6 - - + +
363B ASP* 3.0 35.3 + - - +
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Residues in contact with THR 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142B HIS* 3.9 28.7 + - + +
356B GLY 2.7 20.8 + - - -
357B SER 3.2 7.8 + - - -
359B PRO* 1.3 76.2 - - - +
361B ILE* 1.3 64.5 + - - +
363B ASP* 3.3 9.7 + - - +
364B LEU* 3.0 23.8 + - + +
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Residues in contact with ILE 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B LEU* 3.8 26.9 - - + -
139B LEU* 4.1 18.6 - - + -
142B HIS* 3.9 29.6 - - + +
143B ILE* 4.8 1.3 - - + -
157B LEU* 3.5 19.1 - - + -
159B LEU* 3.7 28.9 - - + -
352B VAL* 4.2 8.1 - - + -
357B SER 2.8 28.0 + - - +
358B ILE* 3.6 5.8 - - - +
360B THR* 1.3 70.9 - - - +
362B CYS* 1.3 63.8 + - - +
364B LEU* 3.2 10.0 + - + +
365B ALA* 2.9 22.2 + - - +
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Residues in contact with CYS 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B VAL* 3.6 30.3 - - - -
157B LEU* 4.0 13.2 - - - -
358B ILE* 3.0 14.9 + - - +
359B PRO* 3.0 15.2 + - + +
361B ILE* 1.3 77.1 - - - +
363B ASP* 1.3 59.9 + - - +
365B ALA* 3.1 3.7 + - - +
366B ARG* 2.8 63.2 + - - +
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Residues in contact with ASP 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359B PRO* 3.0 18.2 + - - +
360B THR* 3.8 8.3 - - - +
362B CYS* 1.3 81.3 - - - +
364B LEU* 1.3 55.0 + - - +
366B ARG* 3.7 14.3 + - - +
367B THR* 2.6 47.1 + - - +
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Residues in contact with LEU 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310A TRP* 3.5 44.4 - - + +
135B THR* 4.4 21.3 - - + +
138B VAL* 3.9 29.6 - - + +
139B LEU* 3.5 32.3 - - + +
142B HIS* 6.3 0.2 - - - +
159B LEU* 6.2 0.2 - - + -
360B THR* 3.0 15.3 + - + +
361B ILE* 3.2 10.5 - - + +
363B ASP* 1.3 76.4 - - - +
365B ALA* 1.3 59.3 + - + +
367B THR* 3.6 1.7 - - - -
368B PHE* 2.8 32.3 + - + +
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Residues in contact with ALA 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B VAL* 3.3 27.4 - - + -
80B TYR 4.0 3.3 - - - +
81B VAL* 3.6 29.8 - - + -
159B LEU* 3.8 10.5 - - + -
361B ILE 2.9 15.2 + - - +
362B CYS 3.7 0.2 - - - +
364B LEU* 1.3 76.7 - - - +
366B ARG* 1.3 63.5 + - - +
368B PHE* 3.3 3.7 + - - +
369B ALA* 3.0 26.7 + - - +
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Residues in contact with ARG 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B ASP 5.9 3.0 - - - +
78B ILE 5.7 1.2 + - - -
79B VAL* 3.9 19.4 - - + +
362B CYS* 2.8 52.5 + - - +
363B ASP* 3.7 13.8 + - - +
365B ALA* 1.3 73.2 - - - +
367B THR* 1.3 57.1 + - - +
369B ALA* 4.1 5.5 - - - +
370B ARG* 3.3 28.3 + - - +
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Residues in contact with THR 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306A ASN* 3.1 41.1 - - + +
310A TRP* 4.1 10.0 - - + -
363B ASP* 2.6 32.5 + - - +
364B LEU 3.7 2.7 - - - -
366B ARG* 1.3 73.7 - - - +
368B PHE* 1.3 65.8 + - - +
370B ARG* 3.3 29.8 + - - +
371B GLU* 3.1 23.1 + - + +
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Residues in contact with PHE 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307A VAL* 5.6 0.2 - - + -
310A TRP* 3.9 17.7 - + + -
81B VAL* 3.4 28.5 - - + -
82B PRO* 3.2 35.2 - - + -
84B PRO* 3.9 26.5 - - + -
131B PRO* 3.7 21.5 - - + -
132B TYR* 5.5 4.3 - + - -
135B THR* 3.2 28.9 - - + -
364B LEU* 2.8 19.7 + - + +
365B ALA* 3.6 5.6 - - - +
367B THR* 1.3 77.6 - - - +
369B ALA* 1.3 56.3 + - - +
371B GLU* 3.8 0.2 - - - -
372B MET* 2.8 52.3 + - + +
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Residues in contact with ALA 369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B TYR* 4.0 7.6 - - + +
82B PRO* 3.7 30.5 - - + -
365B ALA 3.0 16.6 + - - +
366B ARG* 4.1 6.7 - - - +
368B PHE* 1.3 77.9 - - - +
370B ARG* 1.3 58.6 + - - +
373B GLY* 2.8 29.7 + - - +
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Residues in contact with ARG 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306A ASN* 4.5 8.1 - - - +
366B ARG 3.3 15.9 + - - +
367B THR* 3.3 41.0 + - - +
368B PHE 3.4 0.2 - - - -
369B ALA* 1.3 79.2 - - - +
371B GLU* 1.3 62.5 + - - +
373B GLY 4.8 4.3 - - - +
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Residues in contact with GLU 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305A TYR* 3.5 22.0 - - + -
306A ASN* 3.0 40.6 + - - +
307A VAL* 3.2 35.7 + - - +
86B THR* 3.8 17.8 + - - +
91B LEU* 4.1 11.2 - - + +
367B THR* 3.1 17.4 + - + +
368B PHE 4.0 1.1 - - - +
370B ARG* 1.3 84.0 - - + +
372B MET* 1.3 68.1 + - + +
373B GLY 3.7 1.5 - - - +
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Residues in contact with MET 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307A VAL* 3.3 37.9 - - + -
310A TRP* 4.2 5.4 - - + -
82B PRO* 5.3 0.2 - - - -
83B GLU 4.4 0.2 - - - -
84B PRO* 3.5 16.4 - - + +
85B MET 3.4 8.8 + - - -
86B THR* 3.1 23.2 + - - -
87B TYR* 3.7 28.5 - - + +
91B LEU* 4.0 9.4 - - + -
131B PRO* 4.1 13.0 - - - -
368B PHE* 2.8 52.3 + - + +
371B GLU* 1.3 90.3 - - - +
373B GLY* 1.3 65.2 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il